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- PDB-6j1r: Crystal structure of Candida Antarctica Lipase B mutant - RR -

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Basic information

Entry
Database: PDB / ID: 6j1r
TitleCrystal structure of Candida Antarctica Lipase B mutant - RR
ComponentsLipase B
KeywordsHYDROLASE / CALB
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process
Similarity search - Function
Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lipase B
Similarity search - Component
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsCen, Y.X. / Zhou, J.H. / Wu, Q.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Stereodivergent Protein Engineering of a Lipase To Access All Possible Stereoisomers of Chiral Esters with Two Stereocenters.
Authors: Xu, J. / Cen, Y. / Singh, W. / Fan, J. / Wu, L. / Lin, X. / Zhou, J. / Huang, M. / Reetz, M.T. / Wu, Q.
History
DepositionDec 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Lipase B
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,42812
Polymers66,6272
Non-polymers80110
Water5,783321
1
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7026
Polymers33,3141
Non-polymers3885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12090 Å2
MethodPISA
2
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7266
Polymers33,3141
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.023, 80.670, 73.646
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipase B / CALB


Mass: 33313.590 Da / Num. of mol.: 2 / Mutation: T57A, A89T, Q157L, I189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudozyma antarctica (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41365, triacylglycerol lipase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate 0.1M Tris 7.5 30% PEG3000 3% 2-methyl-2,4-pentadiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 70816 / % possible obs: 99 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 20.977
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.636 / Num. unique obs: 3349

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 1.601→46.509 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.29
RfactorNum. reflection% reflection
Rfree0.2151 3340 5.1 %
Rwork0.1763 --
obs0.1782 65549 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→46.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 0 47 321 5026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184959
X-RAY DIFFRACTIONf_angle_d1.566824
X-RAY DIFFRACTIONf_dihedral_angle_d17.3711794
X-RAY DIFFRACTIONf_chiral_restr0.115787
X-RAY DIFFRACTIONf_plane_restr0.01899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6012-1.6240.29391070.21141688X-RAY DIFFRACTION60
1.624-1.64830.2317980.19541875X-RAY DIFFRACTION67
1.6483-1.6740.26541070.19081999X-RAY DIFFRACTION70
1.674-1.70150.24991220.19222099X-RAY DIFFRACTION76
1.7015-1.73080.24961190.21812269X-RAY DIFFRACTION79
1.7308-1.76230.23931220.20732317X-RAY DIFFRACTION82
1.7623-1.79620.27691340.20982380X-RAY DIFFRACTION84
1.7962-1.83290.25121100.1892510X-RAY DIFFRACTION90
1.8329-1.87270.2221550.19032784X-RAY DIFFRACTION98
1.8727-1.91630.22361370.18582789X-RAY DIFFRACTION99
1.9163-1.96420.21981580.18662827X-RAY DIFFRACTION100
1.9642-2.01730.251560.18662821X-RAY DIFFRACTION100
2.0173-2.07670.22131510.1872800X-RAY DIFFRACTION100
2.0767-2.14370.21751220.18882849X-RAY DIFFRACTION99
2.1437-2.22030.21391790.17522755X-RAY DIFFRACTION99
2.2203-2.30920.22041630.16782789X-RAY DIFFRACTION100
2.3092-2.41430.19891520.17672835X-RAY DIFFRACTION100
2.4143-2.54160.23611260.18052868X-RAY DIFFRACTION100
2.5416-2.70080.23731560.17982801X-RAY DIFFRACTION99
2.7008-2.90930.23211600.19292794X-RAY DIFFRACTION98
2.9093-3.2020.23981660.20032815X-RAY DIFFRACTION100
3.202-3.66520.20361470.17992837X-RAY DIFFRACTION100
3.6652-4.61710.16261410.13662833X-RAY DIFFRACTION99
4.6171-46.52860.16391520.13692875X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -75.1514 Å / Origin y: 19.0727 Å / Origin z: 106.1914 Å
111213212223313233
T0.1087 Å20.0194 Å20.0979 Å2-0.0363 Å2-0.0016 Å2--0.0679 Å2
L0.5281 °20.368 °20.4292 °2-0.6301 °20.3486 °2--0.5152 °2
S0.1306 Å °-0.0762 Å °-0.0907 Å °0.0564 Å °-0.0257 Å °-0.0732 Å °0.1138 Å °-0.0808 Å °-0.0312 Å °
Refinement TLS groupSelection details: all

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